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On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Science for Life Laboratory, SciLifeLab.
2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 17, 175101- p.Article in journal (Refereed) Published
Abstract [en]

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrodinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Theta-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Place, publisher, year, edition, pages
2013. Vol. 138, no 17, 175101- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-203304DOI: 10.1063/1.4801330ISI: 000319289600056OAI: oai:DiVA.org:uu-203304DiVA: diva2:636110
Available from: 2013-07-08 Created: 2013-07-08 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Protein Folding Simulations in Kink Model
Open this publication in new window or tab >>Protein Folding Simulations in Kink Model
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The structure of protein is essentially important for life activities. Proteins can perform their functions only by specific structures. In this thesis, the kink and multi-kink model for protein description are reviewed. It is shown that most of the loop parts in Protein Databank (PDB) can be described by very limited number of kinks within the experimental precision. Furthermore, by applying the model into two well studied real proteins (myoglobin and villin headpiece HP35), it is shown that the multi-kink model gives correct folding pathway and thermal dynamical properties compared with the experimental results for both proteins. In particular, the kink model is computationally inexpensive compared with other existing models. In the last chapter, a new visualization method for the heavy atoms in the side-chain is presented.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 56 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1184
Keyword
protein folding, kink model, soliton
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-232562 (URN)978-91-554-9043-0 (ISBN)
Public defence
2014-11-07, 80101, Ångström Laboratory, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2014-10-14 Created: 2014-09-22 Last updated: 2015-01-23

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Niemi, Antti J.Peng, Xubiao

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